build.xml

   1 <?xml version="1.0"?>
   2 <!--
   3  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   4  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   5  *
   6  * This file is part of Jalview.
   7  *
   8  * Jalview is free software: you can redistribute it and/or
   9  * modify it under the terms of the GNU General Public License
  10  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  18  * The Jalview Authors are detailed in the 'AUTHORS' file.
  19 -->
  20 <project name="jalviewX" default="usage" basedir="."
  21  xmlns:if="ant:if"
  22     xmlns:unless="ant:unless">
  23   <taskdef classpath="${clover.jar}" resource="cloverlib.xml" if:set="clover.jar"/>
  24   <clover-env if:set="clover.jar"/>
  25
  26   <target name="help" depends="usage" />
  27   <target name="usage" depends="init">
  28     <echo message="~~~Jalview Ant build.xml Usage~~~~" />
  29     <echo message="Targets include:" />
  30     <echo message="usage - default target, displays this message" />
  31     <echo message="buildindices - generates JavaHelpSearch from the help files" />
  32     <echo message="build - compiles all necessary files for Application" />
  33     <echo message="makedist - compiles and places all necessary jar files into directory dist" />
  34     <echo message="makefulldist - signs all jar files and builds jnlp file for full distribution" />
  35     <echo message="              this needs a keystore and key."/>
  36     <echo message="              Add -Dtimestamp to timestamp signed jars"/>
  37     <echo message="              -Djalview.keyalg and -Djalview.keydig are SHA1/SHA1withRSA"/>
  38     <echo message="              See docs/building.html for more information." />
  39     <echo message="compileApplet - compiles all necessary files for Applet" />
  40     <echo message="makeApplet - compiles, then packages and obfuscates the Applet" />
  41     <echo message="testng - run jalview's tests via testNG. Default group is '${testng-groups}'" />
  42     <echo message="      you can specify particular test groups as a list via -Dtestng-groups=" />
  43     <echo message="See docs/building.html and the comments in build file for other targets." />
  44     <echo message="note: compile and makeApplet optionally compile/obfuscate applet against a different Java version by specifying -Djava118.home=PathtoJDK/lib which is the lib directory in the JDK install that contains rt.jar " />
  45     <echo message="Useful -D flags: -Ddonotobfuscate will prevent applet obfuscation" />
  46     <echo message="Useful -D flags: -Dclover.jar to specify path to openclover for testng coverage report" />
  47   </target>
  48
  49
  50   <!-- utils is a class path to additional utilities needed for
  51     building docs, jars and webstart stuff -->
  52   <!--
  53         Userdefined build property defaults
  54
  55         wsdl.server list (plus namespace mapping info ???)  - also want
  56                 ... to make this a dynamically generatable property
  57         WebStart Location
  58         Build location - provide a temporary root for speed
  59         jarsigner keystore and info
  60         Jakarta and axis classpath ?
  61         Default argument for starting Jalview (if it exists).
  62
  63 -->
  64
  65   <target name="init">
  66     <path id="axis.classpath">
  67       <!-->
  68       <fileset dir="/usr/local/axis/lib">
  69         <include name="**/*.jar" />
  70       </fileset>
  71       <fileset dir="/usr/local/jakarta-tomcat-5/webapps/axis/WEB-INF/lib">
  72         <include name="**/*.jar"/>
  73         <include name="*.jar"/>
  74       </fileset> -->
  75       </path>
  76
  77     <!-- Jalview Version String displayed by application on startup and used to check for updates -->
  78     <property name="JALVIEW_VERSION" value="DEVELOPMENT" />
  79
  80     <property name="INSTALLATION" value="Source" />
  81
  82     <!-- 2.4 (VAMSAS)" -->
  83     <!-- Include debugging information in javac true or false -->
  84     <property name="javac.debug" value="true" />
  85
  86     <!-- JarSigner Key Store for Webstart Distribution -->
  87     <property name="jalview.keystore" value="./keys/.keystore" />
  88     <!-- Keystore Password -->
  89     <property name="jalview.keystore.pass" value="alignmentisfun" />
  90     <!-- Key Name -->
  91     <property name="jalview.key" value="jalview" />
  92     <!-- Key Password -->
  93     <property name="jalview.key.pass" value="alignmentisfun" />
  94     <!-- time stamp server URL -->
  95     <property name="jalview.tsaurl" value="" />
  96     <!-- locally valid proxy for signing with external time server -->
  97     <property name="proxyPort" value="80"/>
  98     <property name="proxyHost" value="sqid"/>
  99     <!-- key sign/digest algorithms -->
 100     <property name="jalview.keyalg" value="SHA1withRSA" description="key algorithm for signing"/>
 101     <property name="jalview.keydig" value="SHA1" description="algorithm for jar digest"/>
 102
 103     <!-- default TestNG groups to run -->
 104     <property name="testng-groups" value="Functional" />
 105     <!-- Java 9 JVM args -->
 106     <condition property="java9">
 107       <equals arg1="${ant.java.version}" arg2="9"/>
 108     </condition>
 109     <!-- Java 10 JVM args -->
 110     <condition property="java10">
 111       <equals arg1="${ant.java.version}" arg2="10"/>
 112     </condition>
 113     <!-- Java 11 JVM args -->
 114     <condition property="java11">
 115       <equals arg1="${ant.java.version}" arg2="11"/>
 116     </condition>
 117     <echo message="java version is ${ant.java.version}"/>
 118
 119     <!-- Don't change anything below here unless you know what you are doing! -->
 120     <!-- Url path for WebStart in JNLP file -->
 121     <property name="WebStartLocation" value="http://www.jalview.org/webstart" />
 122     <!-- Webstart Image - looked for in resources/images -->
 123     <property name="WebStartImage" value="JalviewLogo_big.png" />
 124     <!-- J2SE version needed for webstart launch -->
 125     <!-- Anne's version needs 1.7 - should rebuild VARNA to java 1.6 for release -->
 126     <property name="j2sev" value="1.7+" />
 127     <!-- Java Compilation settings - source and target javac version -->
 128     <property name="javac.source" value="1.8" />
 129     <property name="javac.target" value="1.8" />
 130
 131     <!-- Permissions for running Java applets and applications. -->
 132     <!-- Defaults are those suitable for deploying jalview webstart www.jalview.org -->
 133     <property name="application.codebase" value="*.jalview.org" />
 134     <!-- and allowing the applet to be deployed from any URL -->
 135     <!-- note - if you want to make sure LiveConnect works without any warnings, please rebuild and sign your applet jar with your own domain included in the codebase/allowable-codebase properties -->
 136     <property name="applet.codebase" value="*.jalview.org *.dundee.ac.uk *" />
 137     <property name="applet.caller-codebase" value="${applet.codebase}" />
 138
 139     <!-- build directory configuration -->
 140     <property name="libDir" value="lib" />
 141     <property name="j11libDir" value="j11lib" />
 142     <property name="resourceDir" value="resources" />
 143     <property name="helpDir" value="help" />
 144     <property name="docDir" value="doc" />
 145     <property name="sourceDir" value="src" />
 146     <property name="schemaDir" value="schemas" />
 147     <property name="outputDir" value="classes" unless:set="clover.jar"/>
 148     <property name="outputDir" value="cloverclasses" if:set="clover.jar"/>
 149     <property name="packageDir" value="dist" />
 150     <property name="outputJar" value="jalview.jar" />
 151     <!-- Jalview Applet JMol Jar Dependency -->
 152     <property name="jmolJar" value="JmolApplet-14.6.4_2016.10.26.jar" />
 153     <property name="varnaJar" value="VARNAv3-93.jar" />
 154     <property name="jsoup" value="jsoup-1.8.1.jar" />
 155     <property name="jsonSimple" value="json_simple-1.1.jar" />
 156     <property name="javaJson" value="java-json.jar" />
 157     <property name="jalviewLiteJar" value="jalviewApplet.jar" />
 158     <property name="reportDir" value="test-reports" />
 159     <property name="testDir" value="test" />
 160     <property name="testOutputDir" value="tests" />
 161     <!-- switch to indicate if we should obfuscate jalviewLite -->
 162     <!-- <property name="donotobfuscate" value="true"/> -->
 163     <!-- switch to exclude associations from generated jnlp files -->
 164     <!-- <property name="nojnlpfileassocs" value="true"/> -->
 165
 166     <!-- Jalview Web Service Clients - see the comments in 'buildextclients' for details -->
 167     <property name="wsdl.File" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred?wsdl" />
 168     <property name="wsdl.Files" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/vamsas?wsdlFiles" />
 169     <property name="wsdl.MsaWS" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/MuscleWS?wsdl" />
 170     <property name="wsdl.MsaWS2" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS?wsdl" />
 171     <property name="WSInterf" value="MsaWS" />
 172     <property name="wsdl.Namespace" value="vamsas" />
 173     <property name="wsdl.ClientNS" value="ext.vamsas" />
 174     <!-- the class path for building the application -->
 175     <path id="build.classpath">
 176       <fileset dir="utils">
 177         <include name="*.jar" />
 178         <include name="**/*.jar" />
 179       </fileset>
 180       <fileset dir="${j11libDir}">
 181         <include name="*.jar" />
 182         <include name="**/*.jar" />
 183       </fileset>
 184       <fileset dir="${libDir}">
 185         <include name="*.jar" />
 186         <include name="**/*.jar" />
 187       </fileset>
 188       <fileset dir="${java.home}/lib">
 189         <include name="plugin.jar" />
 190       </fileset>
 191       <fileset dir="appletlib">
 192         <!-- the JmolApplet includes the JmolApplet console and the application javac seems to always try and build all packages
 193                                 -->
 194         <include name="${jmolJar}" />
 195         <include name="${varnaJar}" />
 196       </fileset>
 197     </path>
 198     <path id="test.classpath">
 199       <pathelement path="${outputDir}" />
 200       <path refid="build.classpath" />
 201     </path>
 202     <property name="source.dist.name" value="${basedir}/jalview-src.tar.gz" />
 203     <!-- The Location of the java 1.1.8 jdk -->
 204     <property name="java118.home" value="${java.home}" />
 205     <!-- jre for 1.4 version -->
 206     <property name="applet.jre.tools" value="${java118.home}/lib/rt.jar" />
 207
 208     <!-- the classpath for building the 1.1 applet -->
 209     <path id="jalviewlite.deps">
 210       <fileset dir="${java118.home}">
 211         <include name="lib/rt.jar" />
 212       </fileset>
 213       <fileset dir="${java.home}/lib">
 214         <include name="plugin.jar" />
 215       </fileset>
 216       <pathelement location="appletlib/${jmolJar}" />
 217       <pathelement location="lib/${varnaJar}" />
 218       <pathelement location="appletlib/${jsoup}" />
 219       <pathelement location="appletlib/${jsonSimple}" />
 220       <pathelement location="appletlib/${javaJson}" />
 221
 222     </path>
 223     <!-- default location for outputting javadoc -->
 224     <property name="javadocDir" value="${packageDir}/javadoc" />
 225   </target>
 226
 227
 228   <taskdef classpath="utils/roxes-ant-tasks-1.2-2004-01-30.jar" resource="com/roxes/tools/ant/taskdefs.properties" />
 229   <target name="buildPropertiesFile" depends="init">
 230     <tstamp prefix="build">
 231       <format property="date" pattern="dd MMMM yyyy" />
 232     </tstamp>
 233     <exec executable="/usr/bin/git" outputproperty="git.commit" failifexecutionfails="false">
 234       <arg value="rev-parse" />
 235       <arg value="--short" />
 236       <arg value="HEAD" />
 237     </exec>
 238     <exec executable="/usr/bin/git" outputproperty="git.branch" failifexecutionfails="false">
 239       <arg value="rev-parse" />
 240       <arg value="--abbrev-ref" />
 241       <arg value="HEAD" />
 242     </exec>
 243     <properties file="${outputDir}/.build_properties">
 244       <header>
 245           ---Jalview Build Details---
 246         </header>
 247       <property name="VERSION" value="${JALVIEW_VERSION}" />
 248       <property name="INSTALLATION" value="${INSTALLATION} git-commit:${git.commit} [${git.branch}]" />
 249       <property name="BUILD_DATE" value="${build.date}" />
 250     </properties>
 251   </target>
 252
 253
 254   <target name="clean" depends="init">
 255     <!-- not efficient yet. -->
 256     <delete dir="${outputDir}" includes="*,**/*" />
 257   </target>
 258
 259   <target name="distclean" depends="init, clean">
 260
 261     <echo message="REMOVING ALL BACKUP/AUTOSAVES!" />
 262     <delete>
 263       <fileset dir=".">
 264         <include name="${outputJar}" />
 265         <include name="#*#" />
 266         <include name="#*.*#" />
 267         <include name="**/#*#" />
 268         <include name="**/#*.*#" />
 269         <include name="*~" />
 270         <include name="*.*~" />
 271         <include name="**/*~" />
 272         <include name="**/*.*~" />
 273       </fileset>
 274     </delete>
 275   </target>
 276
 277   <target name="prepare" depends="init">
 278     <mkdir dir="${outputDir}" />
 279     <copy todir="${outputDir}">
 280       <fileset dir=".">
 281         <include name="${docDir}/**/*.*" />
 282         <include name="${helpDir}/**/*.*" />
 283         <include name="${libDir}/*.jar" />
 284       </fileset>
 285       <fileset dir="${resourceDir}">
 286         <include name="**/*.*" />
 287       </fileset>
 288     </copy>
 289   </target>
 290
 291   <target name="build" depends="prepare">
 292     <!-- not efficient yet. -->
 293     <javac source="${javac.source}" target="${javac.target}" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="build.classpath">
 294       <exclude name="jalview/*applet*" />
 295       <exclude name="jalview/appletgui/**" />
 296       <exclude name="com/stevesoft/**" />
 297     </javac>
 298   </target>
 299
 300
 301   <target name="testclean" depends="init">
 302     <delete dir="${testOutputDir}" includes="*,**/*" />
 303   </target>
 304
 305   <target name="prepareTests" depends="init,testclean">
 306     <mkdir dir="${testOutputDir}" />
 307   </target>
 308
 309   <target name="buildTests" depends="build,buildindices,prepareTests">
 310     <javac source="${javac.source}" target="${javac.target}" srcdir="${testDir}" destdir="${testOutputDir}" debug="${javac.debug}" classpathref="test.classpath" includeantruntime="false">
 311     </javac>
 312   </target>
 313
 314   <taskdef resource="testngtasks" classpath="utils/testnglibs/testng.jar" />
 315
 316   <target name="testng" depends="buildTests">
 317     <testng outputDir="${reportDir}" haltOnFailure="false" groups="${testng-groups}" mode="testng"
 318       verbose="2">
 319       <classpath>
 320         <pathelement location="${testOutputDir}" />
 321         <pathelement location="${clover.jar}" if:set="clover.jar"/>
 322         <path refid="test.classpath" />
 323       </classpath>
 324       <jvmarg value="--module-path=${j11libDir}" if:set="java11"/>
 325       <jvmarg value="--add-modules=java.se.ee" if:set="java9"/>
 326       <jvmarg value="--illegal-access=warn" if:set="java9"/>
 327       <classfileset dir="${testOutputDir}" includes="**/*.class" />
 328     </testng>
 329   </target>
 330
 331   <target name="buildindices" depends="init, prepare" unless="help.uptodate">
 332     <replace value="${JALVIEW_VERSION}">
 333       <replacetoken><![CDATA[$$Version-Rel$$]]></replacetoken>
 334       <fileset dir="${outputDir}/${helpDir}">
 335         <include name="help.jhm" />
 336       </fileset>
 337     </replace>
 338
 339     <java classname="com.sun.java.help.search.Indexer" classpathref="build.classpath" fork="true" dir="${outputDir}/${helpDir}">
 340       <arg line="html" />
 341     </java>
 342   </target>
 343
 344   <target name="preparejnlp" depends="makedist">
 345     <copy todir="${packageDir}">
 346       <fileset dir="${resourceDir}/images">
 347         <include name="${WebStartImage}" />
 348       </fileset>
 349     </copy>
 350
 351     <taskdef classpathref="build.classpath" resource="com/roxes/tools/ant/taskdefs.properties" />
 352
 353     <!-- create a dummy jar which will eventually contain the jnlp template -->
 354     <jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
 355       <fileset dir="${packageDir}">
 356         <include name="jalview.jar" />
 357       </fileset>
 358     </jar>
 359
 360     <mkdir dir="${packageDir}/JNLP-INF" />
 361     <antcall target="writejnlpf">
 362       <param name="jnlpFile" value="${packageDir}/JNLP-INF/APPLICATION-TEMPLATE.JNLP" />
 363       <param name="inih" value="*" />
 364       <param name="maxh" value="*" />
 365     </antcall>
 366
 367     <jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
 368       <fileset dir="${packageDir}">
 369         <include name="JNLP-INF/APPLICATION-TEMPLATE.JNLP" />
 370       </fileset>
 371     </jar>
 372
 373     <antcall target="writejnlpf">
 374       <param name="jnlpFile" value="${packageDir}/jalview_256M.jnlp" />
 375       <param name="inih" value="10M" />
 376       <param name="maxh" value="256M" />
 377     </antcall>
 378     <antcall target="writejnlpf">
 379       <param name="jnlpFile" value="${packageDir}/jalview.jnlp" />
 380       <param name="inih" value="800M" />
 381       <param name="maxh" value="1024M" />
 382     </antcall>
 383
 384     <antcall target="writejnlpf">
 385       <param name="jnlpFile" value="${packageDir}/jalview_1G.jnlp" />
 386       <param name="inih" value="128M" />
 387       <param name="maxh" value="512M" />
 388     </antcall>
 389
 390     <antcall target="writejnlpf">
 391       <param name="jnlpFile" value="${packageDir}/jalview_2G.jnlp" />
 392       <param name="inih" value="800M" />
 393       <param name="maxh" value="1024M" />
 394     </antcall>
 395
 396     <!-- finally, need to postprocess to add in associations at end of 'information' element
 397
 398                         <xslt in="${packageDir}/jalview_noa_1G.jnlp" out="${packageDir}/jalview_1G.jnlp">
 399
 400                 </xslt>
 401
 402
 403                         -->
 404     <!--
 405                                 <association mime-type="application-x/ext-file" extensions="fa"/>
 406         <association mime-type="application-x/ext-file" extensions="fasta"/>
 407         <association mime-type="application-x/ext-file" extensions="mfa"/>
 408         <association mime-type="application-x/ext-file" extensions="fastq"/>
 409         <association mime-type="application-x/ext-file" extensions="blc"/>
 410         <association mime-type="application-x/ext-file" extensions="msf"/>
 411         <association mime-type="application-x/ext-file" extensions="pfam"/>
 412         <association mime-type="application-x/ext-file" extensions="aln"/>
 413         <association mime-type="application-x/ext-file" extensions="pir"/>
 414         <association mime-type="application-x/ext-file" extensions="amsa"/>
 415         <association mime-type="application-x/ext-file" extensions="stk"/>
 416         <association mime-type="application-x/ext-file" extensions="jar"/>-->
 417   </target>
 418
 419   <target name="-jarsignwithtsa" depends="makedist,preparejnlp" if="timestamp" unless="nosign">
 420     <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" sigalg="${jalview.keyalg}" digestalg="${jalview.keydig}"
 421       tsaproxyhost="${proxyHost}" tsaproxyport="${proxyPort}" tsaurl="${jalview.tsaurl}">
 422       <fileset dir="${packageDir}">
 423         <include name="*.jar" />
 424       </fileset>
 425     </signjar>
 426   </target>
 427   <target name="-jarsignnotsa" depends="makedist,preparejnlp" if:blank="timestamp" unless="nosign">
 428     <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" sigalg="${jalview.keyalg}" digestalg="${jalview.keydig}">
 429       <fileset dir="${packageDir}">
 430         <include name="*.jar" />
 431       </fileset>
 432     </signjar>
 433   </target>
 434
 435   <target name="makefulldist" depends="makedist,preparejnlp,-jarsignwithtsa,-jarsignnotsa">
 436     <!-- and sign the jars -->
 437     <!-- the default keystore details might need to be edited here -->
 438   </target>
 439
 440   <target name="runenv" depends="init">
 441     <path id="run.classpath">
 442       <pathelement location="${outputDir}" />
 443       <fileset dir="${outputDir}">
 444         <include name="${libDir}/*.jar" />
 445       </fileset>
 446     </path>
 447     <pathconvert targetos="unix" refid="run.classpath" property="run.classpath" />
 448
 449     <echo>java -classpath ${run.classpath} jalview.bin.Jalview
 450       </echo>
 451   </target>
 452
 453   <target name="-generatejnlpf">
 454     <presetdef name="jnlpf">
 455       <jnlp codebase="${WebStartLocation}">
 456         <information>
 457           <title>Jalview</title>
 458           <vendor>The Barton Group</vendor>
 459           <homepage href="http://www.jalview.org" />
 460           <description>Jalview Multiple Alignment Editor</description>
 461           <description kind="short">Jalview</description>
 462           <icon href="${WebStartImage}" />
 463           <offline_allowed />
 464         </information>
 465         <resources>
 466           <j2se version="1.8+" />
 467           <jar main="true" href="jalview.jar"/>
 468           <fileset dir="${packageDir}">
 469             <exclude name="jalview.jar" />
 470             <include name="*.jar" />
 471             <include name="*_*.jar" />
 472             <exclude name="*quaqua*.jar" />
 473           </fileset>
 474           <property name="jalview.version" value="${JALVIEW_VERSION}" />
 475         </resources>
 476         <resources os="Mac OS X">
 477           <fileset dir="${packageDir}">
 478                  <include name="quaqua-filechooser-only-8.0.jar"/>
 479             <include name="*quaqua64*.jnilib.jar" />
 480           </fileset>
 481         </resources>
 482
 483         <application_desc main_class="jalview.bin.Jalview">
 484         </application_desc>
 485         <security>
 486           <all_permissions />
 487         </security>
 488       </jnlp>
 489     </presetdef>
 490
 491     <jnlpf toFile="${jnlpFile}" />
 492     <!-- add the add-modules j2se attribute for java 9 -->
 493     <replace file="${jnlpFile}" value="j2se version=&quot;1.8+&quot; initial-heap-size=&quot;${inih}&quot; max-heap-size=&quot;${maxh}&quot; java-vm-args=&quot;--add-modules=java.se.ee --illegal-access=warn&quot;">
 494           <replacetoken>j2se version="1.8+"</replacetoken>
 495     </replace>
 496   </target>
 497
 498   <target name="-dofakejnlpfileassoc" depends="-generatejnlpf" if="nojnlpfileassocs">
 499     <echo message="Not adding JNLP File Associations" />
 500   </target>
 501
 502   <target name="-dojnlpfileassoc" depends="-generatejnlpf" unless="nojnlpfileassocs">
 503     <replace file="${jnlpFile}">
 504       <replacetoken>
 505         <![CDATA[</information>]]></replacetoken>
 506       <replacevalue>
 507         <![CDATA[
 508           <association mime-type="application-x/ext-file" extensions="fa" />
 509         <association mime-type="application-x/ext-file" extensions="fasta" />
 510         <association mime-type="application-x/ext-file" extensions="mfa" />
 511         <association mime-type="application-x/ext-file" extensions="fastq" />
 512         <association mime-type="application-x/ext-file" extensions="blc" />
 513         <association mime-type="application-x/ext-file" extensions="msf" />
 514         <association mime-type="application-x/ext-file" extensions="pfam" />
 515         <association mime-type="application-x/ext-file" extensions="aln"/>
 516         <association mime-type="application-x/ext-file" extensions="pir"/>
 517         <association mime-type="application-x/ext-file" extensions="amsa"/>
 518         <association mime-type="application-x/ext-file" extensions="stk"/>
 519         <association mime-type="application-x/ext-file" extensions="jvp"/>
 520       </information>]]></replacevalue>
 521   </replace>
 522   <echo message="Added file associations to JNLP file" />
 523 </target>
 524 <target name="writejnlpf" depends="-dojnlpfileassoc,-dofakejnlpfileassoc">
 525 </target>
 526
 527 <target name="buildextclients" depends="init">
 528   <input message="Building external client source from WSDLs - Do you really want to do this ? (Yy/Nn)" validargs="Y,y,n,N" defaultvalue="N" addproperty="doextbuild.response" />
 529   <condition property="dontextbuild">
 530     <equals arg1="n" arg2="${doextbuild.response}" />
 531   </condition>
 532   <condition property="dontextbuild">
 533     <equals arg1="N" arg2="${doextbuild.response}" />
 534   </condition>
 535   <fail if="dontextbuild">
 536         Build External Client Code process aborted by user. Jalview source is unchanged.
 537       </fail>
 538   <!-- Currently, this doesn't happen automatically.
 539      1. Run WSDL2Java as below, which generates an ext.vamsas +
 540      vamsas.<datapackages> fileset.
 541      2. refactor ext.vamsas.SpecificserviceWS* to
 542      ext.vamsas.ServiceclassWS* that implements the ServiceclassWSI interface.
 543      3. Update the jalview.ws.*WServices classes to reflect the
 544      interface type, and all locations of this wsdl type that Jalview
 545      might be using.
 546
 547 -->
 548   <path id="axisbuild">
 549     <path refid="build.classpath" />
 550   </path>
 551   <taskdef resource="axis-tasks.properties" classpathref="axisbuild" />
 552   <move todir="./bak">
 553     <fileset dir="${sourceDir}" id="client">
 554       <include name="${wsdl.ClientNS}/*.*" />
 555     </fileset>
 556   </move>
 557
 558   <axis-wsdl2java output="${sourceDir}" verbose="true" url="${wsdl.MsaWS2}" serverside="false" deployscope="Request" debug="false" helpergen="true" all="true">
 559     <mappingSet>
 560       <mapping namespace="${wsdl.Namespace}" package="${wsdl.ClientNS}" />
 561       <mapping namespace="http://dataTypes.vamsas" package="${wsdl.ClientNS}" />
 562     </mappingSet>
 563   </axis-wsdl2java>
 564 </target>
 565
 566 <target name="makedist" depends="build, buildPropertiesFile, linkcheck, buildindices">
 567   <fail if="clover.jar">
 568     Ignoring request to build jalview distribution with clover-instrumented classes
 569   </fail>
 570   <!-- make the package jar if not already existing -->
 571   <mkdir dir="${packageDir}" />
 572   <!-- clean dir if it already existed -->
 573   <delete>
 574     <fileset dir="${packageDir}">
 575       <include name="*.jar" />
 576     </fileset>
 577   </delete>
 578   <jar destfile="${packageDir}/${outputJar}" index="true">
 579     <manifest>
 580       <attribute name="Main-Class" value="jalview.bin.Jalview" />
 581       <attribute name="Permissions" value="all-permissions" />
 582       <attribute name="Application-Name" value="Jalview Desktop" />
 583       <attribute name="Codebase" value="${application.codebase}" />
 584     </manifest>
 585     <fileset dir="${outputDir}/">
 586       <exclude name="cache*/**" />
 587       <exclude name="*.jar" />
 588       <exclude name="*.jar.*" />
 589       <exclude name="**/*.jar" />
 590       <exclude name="**/*.jar.*" />
 591     </fileset>
 592   </jar>
 593
 594   <copy toDir="${packageDir}" flatten="true">
 595     <fileset dir="${outputDir}">
 596       <include name="*.jar" />
 597       <include name="**/*.jar" />
 598     </fileset>
 599   </copy>
 600 </target>
 601
 602
 603 <!-- jalopy code reformatter -->
 604 <target name="sourcescrub" depends="init,build">
 605   <jalopy destdir="jsrc" classpathref="run.classpath" convention="jalview-jalopy.xml">
 606     <fileset dir="${sourceDir}">
 607       <include name="*.java" />
 608       <include name="**/*.java" />
 609       <include name="**/**/*.java" />
 610     </fileset>
 611   </jalopy>
 612 </target>
 613
 614
 615
 616 <!-- Compile, package and obfuscate Jalview Applet -->
 617 <target name="makeApplet" depends="obfuscate" description="assemble the final jalviewLite applet jar with or without obfuscation" />
 618
 619 <target name="compileApplet" depends="init,clean">
 620   <mkdir dir="${outputDir}" />
 621   <javac source="${javac.source}" target="${javac.target}" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="jalviewlite.deps" includes="jalview/appletgui/**" excludes="ext/**,gui/**,jbgui/**,MCview/**,org/**,vamsas/**,jalview/ext/rbvi/**,jalview/ext/paradise/**,jalview/ext/ensembl/**,jalview/ext/so/**" />
 622 </target>
 623
 624 <target name="packageApplet" depends="compileApplet, buildPropertiesFile">
 625   <copy file="${resourceDir}/images/link.gif" toFile="${outputDir}/images/link.gif" />
 626   <copy todir="${outputDir}/lang">
 627     <fileset dir="${resourceDir}/lang">
 628       <include name="**.*" />
 629     </fileset>
 630   </copy>
 631   <jar destfile="in.jar" index="true">
 632     <manifest>
 633       <attribute name="Main-Class" value="jalview.bin.JalviewLite" />
 634       <attribute name="Application-Name" value="JalviewLite" />
 635       <attribute name="Codebase" value="${applet.codebase}" />
 636     </manifest>
 637     <fileset dir="${outputDir}">
 638       <include name="com/**" />
 639       <include name="MCview/**" />
 640       <include name="jalview/**" />
 641       <include name=".build_properties" />
 642       <include name="images/link.gif" />
 643       <include name="lang/**" />
 644     </fileset>
 645   </jar>
 646 </target>
 647 <target name="obfuscate" depends="-obfuscatefake,-obfuscatereally">
 648 </target>
 649 <target name="-obfuscatefake" depends="packageApplet" if="donotobfuscate">
 650   <copy file="in.jar" tofile="${jalviewLiteJar}" overwrite="true" />
 651   <delete file="in.jar" />
 652 </target>
 653 <target name="-obfuscatereally" unless="donotobfuscate">
 654
 655   <path id="obfuscateDeps.path">
 656     <pathelement location="${applet.jre.tools}" />
 657     <pathelement location="appletlib/${jmolJar}" />
 658     <pathelement location="lib/${varnaJar}" />
 659     <pathelement location="appletlib/${jsoup}" />
 660     <pathelement location="appletlib/${jsonSimple}" />
 661     <pathelement location="appletlib/${javaJson}" />
 662     <fileset dir="${java.home}/lib">
 663       <include name="plugin.jar" />
 664     </fileset>
 665   </path>
 666   <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard_5.3.3.jar" />
 667
 668   <proguard verbose="true" >
 669     <injar file="in.jar" />
 670     <outjar file="${jalviewLiteJar}" />
 671     <libraryjar refid="obfuscateDeps.path" />
 672     <dontwarn />
 673     <keep access="public" type="class" name="jalview.bin.JalviewLite">
 674       <field access="public" />
 675       <method access="public" />
 676       <constructor access="public" />
 677     </keep>
 678     <keep access="public" type="class" name="jalview.appletgui.AlignFrame">
 679       <field access="public" />
 680       <method access="public" />
 681       <constructor access="public" />
 682     </keep>
 683
 684     <keep name="jalview.json.binding**">
 685       <constructor/>
 686       <method name="*"/>
 687     </keep>
 688
 689     <keep access="public" type="class" name="MCview.PDBfile">
 690       <field access="public" />
 691       <method access="public" />
 692       <constructor access="public" />
 693     </keep>
 694
 695     <keep access="public" type="class" name="jalview.ws.jws1.Annotate3D">
 696       <field access="public" />
 697       <method access="public" />
 698       <constructor access="public" />
 699     </keep>
 700
 701     <keep access="public" type="class" name="jalview.ext.jmol.JmolParser">
 702       <field access="public" />
 703       <method access="public" />
 704       <constructor access="public" />
 705     </keep>
 706
 707
 708     <!--      -libraryjars "${obfuscateDeps}"
 709       -injars      in.jar
 710       -outjars     jalviewApplet.jar
 711       -keep public class jalview.bin.JalviewLite
 712        { public * ; } -->
 713   </proguard>
 714   <delete file="in.jar" />
 715 </target>
 716
 717 <target name="sourcedist" description="create jalview source distribution" depends="init">
 718   <delete file="${source.dist.name}" />
 719   <!-- temporary copy of source to update timestamps -->
 720   <copy todir="_sourcedist">
 721     <fileset dir=".">
 722       <exclude name=".*" />
 723       <exclude name="**/.*" />
 724       <exclude name="*.class" />
 725       <exclude name="**/*.class" />
 726       <include name="LICENSE" />
 727       <include name="README" />
 728       <include name="build.xml" />
 729       <include name="jalview-jalopy.xml" />
 730       <include name="JalviewApplet.jpx" />
 731       <include name="JalviewX.jpx" />
 732       <include name="nbbuild.xml" />
 733       <include name="nbproject/genfiles.properties" />
 734       <include name="nbproject/project.properties" />
 735       <include name="nbproject/project.xml" />
 736       <include name="${sourceDir}/*.java" />
 737       <include name="${sourceDir}/**/*.java" />
 738       <include name="${sourceDir}/**/*.cdr" />
 739       <include name="${libDir}/**/*" />
 740       <include name="${resourceDir}/**/*" />
 741       <include name="${helpDir}/**/*" />
 742       <include name="appletlib/${jmolJar}" />
 743       <include name="appletlib/${jsonSimple}" />
 744       <include name="appletlib/${javaJson}" />
 745       <exclude name="**/*locales" />
 746       <exclude name="*locales/**" />
 747       <exclude name="utils/InstallAnywhere/**Build.iap_xml" />
 748       <exclude name="utils/InstallAnywhere/**Build*/**" />
 749       <exclude name="utils/InstallAnywhere/**Build*/**" />
 750       <exclude name="utils/InstallAnywhere/.build*.*/**" />
 751       <exclude name="utils/InstallAnywhere/**locale*" />
 752       <exclude name="utils/InstallAnywhere/**locale*/**" />
 753       <exclude name="utils/InstallAnywhere/**locale*/**" />
 754       <include name="${schemaDir}/**/*" />
 755       <include name="utils/**/*" />
 756       <include name="${docDir}/**/*" />
 757       <include name="examples/**/*" />
 758     </fileset>
 759   </copy>
 760
 761   <tstamp prefix="build">
 762     <format property="year" pattern="yyyy" />
 763   </tstamp>
 764   <!-- each replacetoken CDATA body must be on one line -
 765        otherwise the pattern doesn't match -->
 766   <replace value="${JALVIEW_VERSION}">
 767     <replacetoken><![CDATA[$$Version-Rel$$]]></replacetoken>
 768     <fileset dir="_sourcedist">
 769       <include name="**/*" />
 770     </fileset>
 771   </replace>
 772   <replace dir="_sourcedist" value="${build.year}">
 773     <replacetoken><![CDATA[$$Year-Rel$$]]></replacetoken>
 774     <fileset dir="_sourcedist">
 775       <include name="**/*" />
 776     </fileset>
 777   </replace>
 778
 779   <tar destfile="${source.dist.name}" compression="gzip">
 780     <tarfileset dir="_sourcedist/" prefix="jalview" preserveLeadingSlashes="true">
 781     </tarfileset>
 782   </tar>
 783
 784   <delete dir="_sourcedist" />
 785 </target>
 786 <target name="prepubapplet_1" depends="makeApplet">
 787   <copy todir="${packageDir}/examples">
 788     <fileset dir="examples">
 789       <include name="**/*" />
 790       <include name="javascript/*" />
 791       <include name="jmol/*" />
 792     </fileset>
 793     <fileset dir=".">
 794       <include name="${jalviewLiteJar}" />
 795     </fileset>
 796     <fileset dir="appletlib">
 797       <include name="**/*" />
 798     </fileset>
 799   </copy>
 800   <jar update="true" index="true" jarfile="${packageDir}/examples/${jalviewLiteJar}" />
 801   <jar update="true" index="true" jarfile="${packageDir}/examples/${javaJson}" />
 802   <jar update="true" index="true" jarfile="${packageDir}/examples/${jsonSimple}" />
 803   <jar update="true" index="true" jarfile="${packageDir}/examples/${jmolJar}">
 804     <manifest>
 805       <attribute name="Application-Name" value="Jmol (bundled with JalviewLite)" />
 806       <!--          <attribute name="Permissions" value="sandbox" /> -->
 807       <!--<attribute name="Trusted-Lib" value="true" /> -->
 808       <attribute name="Codebase" value="${applet.codebase}" />
 809       <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
 810     </manifest>
 811   </jar>
 812
 813   <presetdef name="ap_applet.jar">
 814     <!-- build a signed applet with 'all-permissions' -
 815                           Needs 'param name="permissions' value="all-permissions"' in applet tag
 816                           JalviewLite+JmolApplet linked sequence/structure fails
 817                           Mixed code warnings are raised
 818                           -->
 819     <jar update="true" index="true">
 820       <manifest>
 821         <attribute name="Application-Name" value="JalviewLite" />
 822         <attribute name="Permissions" value="all-permissions" />
 823         <attribute name="Codebase" value="${applet.codebase}" />
 824         <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
 825         <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
 826       </manifest>
 827     </jar>
 828   </presetdef>
 829   <presetdef name="applet.jar">
 830     <!-- build signed applet with sandbox permissions -
 831                           Needs 'param name="permissions' value="sandbox"' in applet tag
 832                          Preserves Pre-Java 1.7_u45 behavior once 'permissions' parameter added to applet tag
 833                         -->
 834
 835     <jar update="true" index="true">
 836       <manifest>
 837         <attribute name="Application-Name" value="JalviewLite" />
 838         <attribute name="Permissions" value="sandbox" />
 839         <attribute name="Codebase" value="${applet.codebase}" />
 840         <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
 841         <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
 842       </manifest>
 843     </jar>
 844   </presetdef>
 845   <presetdef name="tl_applet.jar">
 846     <!-- build signed applet with trusted library/trusted permissions -
 847                                 Needs 'param name="permissions' value="all-permissions"' in applet tag
 848                                j1.7_45:
 849                                No mixed code warnings raised
 850                                Jmol/JalviewLite sequence/structure example doesn't link structures
 851                                Raises dialog asking user to allow page to control applet via LiveConnect javascript
 852
 853                               -->
 854
 855     <jar update="true" index="true">
 856       <manifest>
 857         <attribute name="Application-Name" value="JalviewLite" />
 858         <attribute name="Permissions" value="all-permissions" />
 859         <attribute name="Codebase" value="${applet.codebase}" />
 860         <attribute name="Trusted-Only" value="true" />
 861         <attribute name="Trusted-Library" value="true" />
 862       </manifest>
 863     </jar>
 864   </presetdef>
 865   <presetdef name="to_applet.jar">
 866     <!-- not fully test variant (yet) -->
 867     <jar update="true" index="true">
 868       <manifest>
 869         <attribute name="Application-Name" value="JalviewLite" />
 870         <attribute name="Permissions" value="all-permissions" />
 871         <attribute name="Codebase" value="${applet.codebase}" />
 872         <attribute name="Trusted-Only" value="true" />
 873       </manifest>
 874     </jar>
 875   </presetdef>
 876   <!-- create differently privileged artefacts -->
 877   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/u_${jalviewLiteJar}" />
 878   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true" />
 879   <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/u_${javaJson}" overwrite="true" />
 880   <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/u_${jsonSimple}" overwrite="true" />
 881   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/ap_${jalviewLiteJar}" />
 882   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/ap_${jmolJar}" />
 883   <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/ap_${javaJson}" />
 884   <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/ap_${jsonSimple}" />
 885   <ap_applet.jar jarfile="${packageDir}/examples/ap_${jalviewLiteJar}" />
 886   <ap_applet.jar jarfile="${packageDir}/examples/ap_${jmolJar}" />
 887   <ap_applet.jar jarfile="${packageDir}/examples/ap_${javaJson}" />
 888   <ap_applet.jar jarfile="${packageDir}/examples/ap_${jsonSimple}" />
 889   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/tl_${jalviewLiteJar}" />
 890   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/tl_${jmolJar}" />
 891   <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/tl_${javaJson}" />
 892   <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/tl_${jsonSimple}" />
 893   <tl_applet.jar jarfile="${packageDir}/examples/tl_${jalviewLiteJar}" />
 894   <tl_applet.jar jarfile="${packageDir}/examples/tl_${jmolJar}" />
 895   <tl_applet.jar jarfile="${packageDir}/examples/tl_${javaJson}" />
 896   <tl_applet.jar jarfile="${packageDir}/examples/tl_${jsonSimple}" />
 897   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/to_${jalviewLiteJar}" />
 898   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/to_${jmolJar}" />
 899   <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/to_${javaJson}" />
 900   <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/to_${jsonSimple}" />
 901   <to_applet.jar jarfile="${packageDir}/examples/to_${jalviewLiteJar}" />
 902   <to_applet.jar jarfile="${packageDir}/examples/to_${jmolJar}" />
 903   <to_applet.jar jarfile="${packageDir}/examples/to_${javaJson}" />
 904   <to_applet.jar jarfile="${packageDir}/examples/to_${jsonSimple}" />
 905   <!-- finally, create manifest for original jars -->
 906   <applet.jar jarfile="${packageDir}/examples/${jalviewLiteJar}" />
 907   <applet.jar jarfile="${packageDir}/examples/${jmolJar}" />
 908   <applet.jar jarfile="${packageDir}/examples/${javaJson}" />
 909   <applet.jar jarfile="${packageDir}/examples/${jsonSimple}" />
 910
 911   <!-- todo - write examples/downloads for alternate versions of the applet
 912     probably don't need to do this now since we don't have alternate versions anymore !-->
 913 </target>
 914 <target name="-signapplet" depends="prepubapplet_1">
 915   <fileset id="signappletjarset" dir="${packageDir}/examples">
 916     <exclude name="u_*.jar" />
 917     <include name="${jalviewLiteJar}" />
 918     <include name="${jmolJar}" />
 919     <include name="${javaJson}" />
 920     <include name="${jsonSimple}" />
 921     <include name="to_${jalviewLiteJar}" />
 922     <include name="to_${jmolJar}" />
 923     <include name="to_${javaJson}" />
 924     <include name="to_${jsonSimple}" />
 925     <include name="tl_${jalviewLiteJar}" />
 926     <include name="tl_${jmolJar}" />
 927     <include name="tl_${javaJson}" />
 928     <include name="tl_${jsonSimple}" />
 929     <include name="ap_${jalviewLiteJar}" />
 930     <include name="ap_${jmolJar}" />
 931     <include name="ap_${javaJson}" />
 932     <include name="ap_${jsonSimple}" />
 933   </fileset>
 934 </target>
 935 <target name="-signappletnotsa" if:blank="timestamp" depends="-signapplet" unless="nosign">
 936   <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
 937     <fileset refid="signappletjarset" />
 938   </signjar>
 939 </target>
 940
 941 <target name="-signapplettsa" if="timestamp" depends="-signapplet" unless="nosign">
 942   <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" tsaproxyhost="${proxyHost}" tsaproxyport="${proxyPort}" tsaurl="${jalview.tsaurl}">
 943     <fileset refid="signappletjarset" />
 944   </signjar>
 945 </target>
 946
 947 <target name="signApplet" description="internal target to sign applet" depends="-signappletnotsa,-signapplettsa" />
 948
 949 <target name="pubapplet" description="installs the jalviewLite applet and dependent jars into an applet examples directory built under ${outputDir}" depends="makeApplet, signApplet">
 950
 951   <!-- bizarre bug causes JmolApplet to always get signed, even if excluded from above. so copy explicitly -->
 952   <copy file="appletlib/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true" />
 953   <copy file="appletlib/${jsonSimple}" tofile="${packageDir}/examples/u_${jsonSimple}" overwrite="true" />
 954   <copy file="appletlib/${javaJson}" tofile="${packageDir}/examples/u_${javaJson}" overwrite="true" />
 955   <!-- finally, replace any launchApp servlet tags with a version specification -->
 956   <replace value="http://www.jalview.org/services/launchApp?version=${JALVIEW_VERSION}&quot;">
 957     <replacetoken>
 958       <![CDATA[http://www.jalview.org/services/launchApp"]]>
 959     </replacetoken>
 960     <fileset dir="${packageDir}/examples">
 961       <include name="**/*.html" />
 962     </fileset>
 963   </replace>
 964   <replace value="http://www.jalview.org/services/launchApp?version=${JALVIEW_VERSION}'">
 965     <replacetoken>
 966       <![CDATA[http://www.jalview.org/services/launchApp']]>
 967     </replacetoken>
 968     <fileset dir="${packageDir}/examples">
 969       <include name="**/*.html" />
 970     </fileset>
 971   </replace>
 972
 973 </target>
 974 <target name="sourcedoc" description="Create jalview source documentation pages" depends="init">
 975   <javadoc destdir="${javadocDir}">
 976     <packageset dir="${sourceDir}" includes="jalview/*,MCView/*">
 977     </packageset>
 978   </javadoc>
 979 </target>
 980 <target name="linkcheck" depends="init,prepare">
 981   <javac srcdir="utils" destdir="utils" includes="HelpLinksChecker.java"/>
 982   <java fork="true" dir="${helpDir}" classpath="utils" classname="HelpLinksChecker" failonerror="true">
 983     <arg file="${helpDir}"/>
 984     <arg value="-nointernet"/>
 985   </java>
 986 </target>
 987 </project>